Sequence
atgc intronic sequence ATGC exonic sequence...catactattttatattttgacattagatgtactcaattctttatccttgttcaactgtgctatgcttgatttaatttttgctttgctgcttcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC
Basic information
species | Glycine max |
transcript | GLYMA09G23980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 2
---catactattttatattttgacattagatgtactcaattctttatccttgttcaactgtgctatgcttg-atttaatttttgctttgctgcttcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC
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gttagtggcactcttcattttttcaataaaagttatacatgaacactcccataacccctctgctacatttttatctatgtactaagttatttctt-gtttgcagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTGGGTTCTTCTTATGCATCAGGCGATTCAAGGTTTGCTCGTCTATTG
upper sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 2
---catactattttatattttgacattagatgtactcaattctttatccttgttcaactgtgctatgcttgatttaatttttgctttgctgcttcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC
|| | | ||||| |||| | || || ||| | || || ||||| || || || | | | | || || |||| |||| ||||| |||||||| ||||| ||||||||||||||||||| ||| | ||| | || | | |||| | | ||||||||| | | | |
gttagcgttactcttcatttttcaattaaagttatacatgaacacttccataatcccctctgctacattttatctatgtaataagtaatttatt-gtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTG
upper sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 2
--------ca-tactattttatattttgacattagat-gtactcaattctttatccttgttcaactgtgctatgcttgatttaatttttgctttgctgcttcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC
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ctctgaatcactgttgtcttatgtttttaccttttttagcagtcctcttttagcacttccccagtaatttcat--ttaattca-ttttttttttgtt-------tcacagCACTGCATGTATGAAGCTTGAGGAATATCAAACTGCTAAGGCAGCCTTCGAAACAGGGGCTTCCTTGGCACCGGGAGATTCAAGATTCACTAATTTGATAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|10238957|gb|BE807845.1|BE807845EST: AAAGCAATTGAATTGAATCCTTCTCTACCAAAAGCATATTTGCGGAAAGG TACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGA
genomic: AAAGCAATTGAATTGAATCCTTCTCTACCAAAAGCATATTTGCGGAAAGGgtaagtacca ... tcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGA
EST:
gi|15816108|gb|BI788383.1|BI788383EST: AAAGCAATTGAATTGAATCCTTCTCTACCAAAAGCATATTTGCGGAAAGG TACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGA
genomic: AAAGCAATTGAATTGAATCCTTCTCTACCAAAAGCATATTTGCGGAAAGGgtaagtacca ... tcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgttcaactgtgctatgcttgatttaatttttgctttgctgcttcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC
atttaat putative branch site (score: 4)
ctgcttc putative PPT
atttaatttttgcttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catactattttatattttgacattagatgtactcaattctttatccttgttcaactgtgctatgcttgatttaatttttgctttgctgcttcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC
- - - - - - - - - - - - - - - - - - - - - - -cttgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - aactgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgct